represent sparsified data of RNA ensemble extended by in loop probabilities More...

#include <ext_rna_data.hh>

Inheritance diagram for LocARNA::ExtRnaData:

Collaboration diagram for LocARNA::ExtRnaData:

[legend]

Public Member Functions
	ExtRnaData (const RnaEnsemble &rna_ensemble, double p_bpcut, double p_bpilcut, double p_uilcut, double max_bps_length_ratio, double max_uil_length_ratio, double max_bpil_length_ratio, const PFoldParams &pfoldparams)
	Construct from RnaEnsemble with cutoff probability. More...

	ExtRnaData (const std::string &filename, double p_bpcut, double p_bpilcut, double p_uilcut, double max_bps_length_ratio, double max_uil_length_ratio, double max_bpil_length_ratio, const PFoldParams &pfoldparams)
	Construct from input file. More...

	~ExtRnaData ()
	destructor

double	arc_in_loop_cutoff_prob () const
	Get base pair in loop cutoff probability. More...

double	arc_in_loop_prob (pos_type i, pos_type j, pos_type p, pos_type q) const
	Get base pair in loop probability. More...

double	arc_external_prob (pos_type i, pos_type j) const
	Get base pair in loop probability. More...

double	unpaired_in_loop_cutoff_prob () const
	Get unpaired base in loop cutoff probability. More...

double	unpaired_in_loop_prob (pos_type k, pos_type p, pos_type q) const
	Get base pair in loop probability. More...

double	unpaired_external_prob (pos_type k) const
	Get base pair in loop probability. More...

std::ostream &	write_size_info (std::ostream &out) const
	Write object size information. More...

std::ostream &	write_pp (std::ostream &out, double p_outbpcut=0, double p_outbpilcut=0, double p_outuilcut=0) const

Public Member Functions inherited from LocARNA::RnaData
	RnaData (const RnaEnsemble &rna_ensemble, double p_bpcut, double max_bps_length_ratio, const PFoldParams &pfoldparams)
	Construct from RnaEnsemble with cutoff probability. More...

	RnaData (const std::string &filename, double p_bpcut, double max_bps_length_ratio, const PFoldParams &pfoldparams)
	Construct from file. More...

	RnaData (const RnaData &rna_dataA, const RnaData &rna_dataB, const Alignment &alignment, double p_expA, double p_expB, bool only_local=false)
	Construct as consensus of two aligned RNAs. More...

virtual	~RnaData ()
	destructor

const Sequence &	sequence () const
	Get the multiple alignment as sequence. More...

const MultipleAlignment &	multiple_alignment () const
	Get the multiple alignment. More...

size_type	length () const
	Get the sequence length. More...

double	arc_cutoff_prob () const
	Get base pair cutoff probability. More...

double	arc_prob (pos_type i, pos_type j) const
	Get arc probability. More...

std::string	mea_structure (double gamma=1.) const
	maximum expected accuracy structure More...

vrna_plist_t *	plist () const
	Construct plist (pair list of Vienna RNA) More...

double	joint_arc_prob (pos_type i, pos_type j) const
	Get arc probability. More...

double	stacked_arc_prob (pos_type i, pos_type j) const
	Get arc probability. More...

double	prob_paired_upstream (pos_type i) const
	Probability that a position is paired upstream. More...

double	prob_paired_downstream (pos_type i) const
	Probability that a position is paired downstream. More...

double	prob_unpaired (pos_type i) const
	Unpaired probability. More...

std::ostream &	write_pp (std::ostream &out, double p_outbpcut=0) const

std::ostream &	write_size_info (std::ostream &out) const
	Write object size information. More...

bool	has_stacking () const
	Availability of stacking terms. More...

void	set_anchors (const SequenceAnnotation &anchors)
	Write access to alignment anchors. More...

Protected Member Functions
virtual std::istream &	read_pp (std::istream &in)

virtual void	init_from_fixed_structure (const SequenceAnnotation &structure, bool stacking)
	initialize from fixed structure More...

virtual void	init_from_rna_ensemble (const RnaEnsemble &rna_ensemble, const PFoldParams &pfoldparams)
	initialize from rna ensemble More...

virtual bool	inloopprobs_ok () const
	check in loop probabilities More...

Protected Member Functions inherited from LocARNA::RnaData
	RnaData (double p_bpcut)
	Almost empty constructor. More...

arc_probs_const_iterator	arc_probs_begin () const
	begin of arcs with probability above cutoff Supports iteration over arcs More...

arc_probs_const_iterator	arc_probs_end () const
	begin of arcs with probability above cutoff Supports iteration over arcs More...

bool	read_autodetect (const std::string &filename, bool stacking)
	read and initialize from file, autodetect format More...

virtual void	read_pp (const std::string &filename)

void	read_old_pp (const std::string &filename)

void	read_ps (const std::string &filename)

Friends
class	ExtRnaDataImpl

Additional Inherited Members
Public Types inherited from LocARNA::RnaData
typedef SparseMatrix< double >	arc_prob_matrix_t
	arc probability matrix

typedef size_t	size_type
	usual size type

Protected Types inherited from LocARNA::RnaData
typedef arc_prob_matrix_t::const_iterator	arc_probs_const_iterator
	type of constant iterator over arcs with probability above cutoff

Protected Attributes inherited from LocARNA::RnaData
RnaDataImpl *	pimpl_

Detailed Description

represent sparsified data of RNA ensemble extended by in loop probabilities

knows sequence, cutoff probability and base pair probabilities greater than the cutoff probability

Note: This class knows the cutoff probabilities of its data. These cutoffs can be different from the cutoffs in classes like BasePairs which define the structure elements that are considered by algorithms.; put the extension of extended pp format as additional record after the regular pp-data, such that extended pp files can be read as non-extended ones

Constructor & Destructor Documentation

LocARNA::ExtRnaData::ExtRnaData	(	const RnaEnsemble &	rna_ensemble,
		double	p_bpcut,
		double	p_bpilcut,
		double	p_uilcut,
		double	max_bps_length_ratio,
		double	max_uil_length_ratio,
		double	max_bpil_length_ratio,
		const PFoldParams &	pfoldparams
	)

Construct from RnaEnsemble with cutoff probability.

Parameters

rna_ensemble	RNA ensemble data
p_bpcut	cutoff probability for base pairs
p_bpilcut	cutoff probability for base pairs in loops
p_uilcut	cutoff probability for unpaired bases in loops
pfoldparams	parameters for partition folding

Note: requires that rnaensemble has in loop probabilities

LocARNA::ExtRnaData::ExtRnaData	(	const std::string &	filename,
		double	p_bpcut,
		double	p_bpilcut,
		double	p_uilcut,
		double	max_bps_length_ratio,
		double	max_uil_length_ratio,
		double	max_bpil_length_ratio,
		const PFoldParams &	pfoldparams
	)

Construct from input file.

Parameters

filename	input file name
p_bpcut	cutoff probability for base pairs
p_bpilcut	cutoff probability for base pairs in loops
p_uilcut	cutoff probability for unpaired bases in loops
pfoldparams	parameters for partition folding

Note: autodetect format of input; for fa or aln input formats, predict base pair probabilities

Member Function Documentation

double LocARNA::ExtRnaData::arc_external_prob	(	pos_type	i,
		pos_type	j
	)		const

Get base pair in loop probability.

Parameters

i	left sequence position
j	right sequence position

Returns: probability of basepair (i,j) in external loop if above threshold; otherwise, 0

double LocARNA::ExtRnaData::arc_in_loop_cutoff_prob ( ) const

Get base pair in loop cutoff probability.

Returns: cutoff probability p_bpcut

double LocARNA::ExtRnaData::arc_in_loop_prob	(	pos_type	i,
		pos_type	j,
		pos_type	p,
		pos_type	q
	)		const

Get base pair in loop probability.

Parameters

i	left sequence position of inner base pair
j	right sequence position of inner base pair
p	left sequence position of closing base pair
q	right sequence position of closing base pair

Returns: joint probability of basepair (i,j) in loop of (p,q) if above threshold; otherwise, 0

void LocARNA::ExtRnaData::init_from_fixed_structure	(	const SequenceAnnotation &	structure,
		bool	stacking
	)

protectedvirtual

initialize from fixed structure

Parameters

structure	fixed structure
stacking	whether to initialize stacking terms

Note: overloaded to initialize with additional information (in loop probabilities)

Reimplemented from LocARNA::RnaData.

void LocARNA::ExtRnaData::init_from_rna_ensemble	(	const RnaEnsemble &	rna_ensemble,
		const PFoldParams &	pfoldparams
	)

protectedvirtual

initialize from rna ensemble

Parameters

rna_ensemble	rna ensemble
stacking	whether to initialize stacking terms

Note: overloaded to initialize with additional information (in loop probabilities)

Precondition: bp cutoff prob is initialized

Reimplemented from LocARNA::RnaData.

bool LocARNA::ExtRnaData::inloopprobs_ok ( ) const

protectedvirtual

check in loop probabilities

Returns: true iff loop probabilities are available or not required

Note: use to indicate the need for recomputation in read_autodetect(); always true in RnaData

Reimplemented from LocARNA::RnaData.

std::istream & LocARNA::ExtRnaData::read_pp ( std::istream & in )

protectedvirtual

Read data in pp format 2.0 with in-loop probabilities

Parameters

in	input stream

See also: RnaData::read_pp()

Reimplemented from LocARNA::RnaData.

double LocARNA::ExtRnaData::unpaired_external_prob ( pos_type k ) const

Get base pair in loop probability.

Parameters

k	sequence position (unpaired base)

Returns: probability of base k unpaired in external loop if above threshold; otherwise, 0

double LocARNA::ExtRnaData::unpaired_in_loop_cutoff_prob ( ) const

Get unpaired base in loop cutoff probability.

Returns: cutoff probability p_bpcut

double LocARNA::ExtRnaData::unpaired_in_loop_prob	(	pos_type	k,
		pos_type	p,
		pos_type	q
	)		const

Get base pair in loop probability.

Parameters

k	sequence position (unpaired base)
p	left sequence position of closing base pair
q	right sequence position of closing base pair

Returns: joint probability of unpaired base k in loop of (p,q) if above threshold; otherwise, 0

std::ostream & LocARNA::ExtRnaData::write_pp	(	std::ostream &	out,
		double	p_outbpcut = `0`,
		double	p_outbpilcut = `0`,
		double	p_outuilcut = `0`
	)		const

Write data in extended pp format

Parameters

out	output stream
p_outbpcut	cutoff probability
p_outbpilcut	cutoff probability base pairs in loop
p_outuilcut	cutoff probability unpaired in loop

Returns: stream

Writes only base pairs with probabilities greater than p_outbpcut; base pairs in loops, p_outbpilcut; unpaired bases in loops, p_outuilcut

std::ostream & LocARNA::ExtRnaData::write_size_info ( std::ostream & out ) const

Write object size information.

Parameters

out	output stream

Writes numbers of stored probabilities to stream

The documentation for this class was generated from the following files:

src/LocARNA/ext_rna_data.hh
src/LocARNA/rna_data.cc

Public Member Functions

Protected Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation